Decoding color variation: genome-wide characterization and expression analysis of pigment pathways in Neocaridina denticulata

Body coloration in crustaceans is a fascinating ecological and evolutionary trait, yet its genetic basis remains poorly understood. The freshwater shrimp Neocaridina denticulata, which possesses diverse color variants, serves as an ideal model for dissecting the molecular mechanisms of crustacean pigmentation. Here, we systematically identified and characterized the core gene repertoire for the carotenoid, melanin and pteridine pigment pathways in N. denticulata and analyzed their expression patterns across strains of different color (red, yellow, blue). Most key genes involved in these pigment pathways were found in N. denticulata, including BCO-like for carotenoid cleavage, GCH1 and PTPS for pteridine synthesis, and TH for melanogenesis, suggesting conserved pigment metabolism and regulation in crustaceans. Furthermore, expression profiling of these key pigment genes across tissues in various color strains revealed distinct color-specific patterns. Within the carotenoid pathway, BCO-like1 showed dominant hepatopancreatic expression, with levels highest in the yellow strain and lowest in the blue strain. BCO-like2 and BCO-like3 were expressed across tissues, with strain-specific high expression in the intestine (red/yellow strain) or epidermis (blue strain). Correspondingly, the abundance of the astaxanthin-binding protein CRCN was significantly lower in the red and yellow strains than in the blue strain. In the pteridine pathway, GCH1 and PTPS exhibited a similar tissue distribution pattern in different strains, with high levels in the hepatopancreas, intestines, and eyestalks. However, their expression levels and pteridine contents were significantly higher in the red and yellow strains than in the blue strains. The melanin pathway gene TH was strongly and specifically expressed in eyestalks, and its level was significantly lower in the blue strain. Together, our findings provide the first comprehensive characterization of pigment pathway components in N. denticulata and demonstrate that the carotenoid and pteridine pigment pathways are major contributors to color variation, particularly distinguishing the blue strain from the red and yellow strains. This study establishes a crucial genetic foundation for understanding the evolution and regulation of crustacean coloration, and offers direct implications for selective breeding in aquaculture.